QTL mapping is an effective method for marker assisted selection (MAS) breeding, and high-density linkage genetic map is necessary for fine mapping of QTLs. In this study, high-density genetic maps were constructed using RAD technology in hybrid Epinephelus fuscoguttatus (female) and Epinephelus tukula (male) progenies. The sex-average linkage map contained 150468 SNPs with an average marker interval of 0.011 cM. In grouper, the linkage map in this study has the largest number of markers and the smallest average marker interval. The sex-average, female-specific and male-specific linkage maps were composed of 24 LGs, which is consistent with their chromosome number. In addition, 24 QTLs comprising 318 SNPs associated with body weight, full length, body length, head length, body height and body thickness were identified based on the bin map. 56 candidate genes were obtained after screening of the genes within the QTL confidence interval. Among them, Gpr126, FAM20A, FAM20C, Sox9b, Foxm1, Foxl1, Myf6, ZBTB38 and SL need to be paid attention. These findings are of great significance to the MAS breeding of the hybrid and its male and female parents.